Smoothies and Sinusoids: Why Fourier Analysis is a Great Tool for Tropical Phenology

Post provided by Emma R. Bush and Nils Bunnefeld

What is Fourier Analysis?

Strictly speaking, Fourier analysis is the decomposition of any mathematical function into a series of sine and cosine waves (sinusoids). But let’s not talk about maths – how about food instead?

The Fourier transform is like a special set of sieves that helps you find out all the ingredients in your favourite smoothie ©VICUSCHKA/Shutterstock.com

The Fourier transform is like a special set of sieves that helps you find out all the ingredients in your favourite smoothie ©VICUSCHKA/Shutterstock.com

Imagine you’ve just bought a delicious smoothie from your local café. You like the smoothie so much that you want to know the recipe so that you can make it again at home whenever you want. You’re too shy to ask at the café, so you pour the smoothie through a series of special sieves that separate out each of the ingredients and you write down the recipe – 100ml orange juice, 50ml mango juice, 50ml banana purée and a handful of hipster kale (we haven’t tried this recipe, but we’re sure it would be lovely). You’re quite keen to keep drinking the smoothie, so you mix all the separated ingredients back together again, and the smoothie is just as delicious as before. Continue reading

Lasers in the Jungle Somewhere: How Airborne LiDAR Reveals the Structure of Forests

Post provided by Phil Wilkes (PDRA, Department of Geography, University College London)

Like an X-ray, airborne LiDAR allows you to peer through the dense canopy, revealing the structure of the forest beneath. ©Robert Kerton, CSIRO

Like an X-ray, airborne LiDAR allows you to peer through the dense canopy, revealing the structure of the forest beneath. ©Robert Kerton, CSIRO

How many samples do you hope to collect on your next field assignment? 50, 100 or 1000? How about billions. It may seem overly optimistic, but that’s the reality when using Light Detection and Ranging, or LiDAR.

LiDAR works on the principle of firing hundreds of thousands of laser pulses a second that measure the distance to an intercepting surface. This harmless barrage of light creates a highly accurate 3D image of the target – whether it’s an elephant, a Cambodian temple or pedestrians walking down the street. LiDAR has made the news over recent years for its ability to unearth ancient temples through thick jungle, but for those of us with an ecological motive it is the otherwise impenetrable cloak of vegetation which is of more interest.

Airborne LiDAR in Forests

As it’s National Tree Week in the UK, the focus of this blog post will be on the application of LiDAR in forests. There are a number of techniques that use LiDAR in forests, across a range of scales, from handheld, backpack and tripod mounted terrestrial laser scanners to spaceborne instruments on the International Space Station. Continue reading

Genetic Research May Help Trace Chum Salmon to Home Rivers

Below is a press release about the Methods paper ‘Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci‘ taken from the University of Alaska Fairbanks.

Michael Garvin sails through Auke Bay, just north of Juneau in Southeast Alaska. ©Chris Lunsford

Michael Garvin sails through Auke Bay, just north of Juneau in Southeast Alaska. ©Chris Lunsford

University of Alaska Fairbanks researchers have uncovered genetic markers that can help trace chum salmon to the rivers in which they hatched, according to a new paper published in the journal Methods in Ecology and Evolution.

Mapping out chum salmon pathways could help improve management of the species in Western Alaska, according to Oregon State University Department of Integrative Biology postdoctoral fellow Michael Garvin.

“In some years, chum salmon are frequently the bycatch of pollock fishermen” in the Bering Sea, Garvin explained. “Genetically, chum salmon that originate in Western Alaska tend to look very similar. This makes it difficult for stakeholders because management and conservation efforts to address this bycatch can differ among these regions, but the ability to identify them with genetics is not possible.” Continue reading

National Tree Week Virtual Issue

mee-nationaltreeweek-cover-720pxlIn the UK, National Tree Week (26 November – 4 December) celebrates tree planting within local communities. The latest BES cross-journal Virtual Issue contains recent papers that highlight the global importance of trees and forests as habitat – for species from insects to primates – and in meeting human needs for fuel and agriculture. The selected papers also demonstrate novel methods scientists are using to study trees and forests.

National Tree Week is the UK’s largest tree celebration. It was started in 1975 by the Tree Council and has grown into an event that brings hundreds of organisations together to mark the beginning of Britain’s winter tree planting season.

This Virtual Issue was compiled by Methods in Ecology and Evolution Associate Editors Sarah Goslee and Sean McMahon. All of the articles in this Virtual Issue are free for a limited time and we have a little bit more information about each of the Methods papers included here:

Connecting Forest Patches

Sagebrush steppe in eastern Idaho, USA

© Brittany J. Teller

Landscape connectivity is important for the ecology and genetics of populations threatened by climate change and habitat fragmentation. To begin our Virtual Issue Rayfield et al. present a method for identifying a multipurpose network of forest patches that promotes both short- and long-range connectivity. Their approach can be tailored to local, regional and continental conservation initiatives to protect essential species movements that will allow biodiversity to persist in a changing climate. The authors illustrate their method in the agroecosystem bordered by the Laurentian and Appalachian mountain ranges, that surrounds Montreal.

Continue reading

Topography of Teeth: Tools to Track Animal and Ecosystem Responses to Environmental Changes

Below is a press release about the Methods paper ‘Inferring diet from dental morphology in terrestrial mammals‘ taken from the Smithsonian Institution.

By charting the slopes and crags on animals’ teeth as if they were mountain ranges, scientists at the Smithsonian’s National Museum of Natural History have created a powerful new way to learn about the diets of extinct animals from the fossil record.

Understanding the diets of animals that lived long ago can tell researchers about the environments they lived in and help them piece together a picture of how the planet has changed over deep time. The new quantitative approach to analysing dentition, reported on 21 November in the journal Methods in Ecology and Evolution, will also give researchers a clearer picture of how animals evolve in response to changes in their environment.

gorilla

A 3D reconstruction of the teeth of a western gorilla (Gorilla gorilla).

Continue reading

In Vivo Micro-CT Scanning: Studying Reptiles and Amphibians from the Inside Out

POST PROVIDED BY CHRIS BROECKHOVEN, ANTON DU PLESSIS, STEPHAN G. LE ROUX, P. LE FRAS N. MOUTON AND CANG HUI

Lizards, such as these South African armadillo lizards, serve an important role as model organisms for various ecological and evolutionary studies. © Chris Broeckhoven

Lizards, such as these South African armadillo lizards, serve an important role as model organisms for various ecological and evolutionary studies. © Chris Broeckhoven

X-ray micro-computed tomography – or µCT – is a technique that uses x-rays to create high resolution cross-sections of samples. Virtual 3D models can be made from these cross-sections without destroying the original samples. Micro-CT has important applications in medical imaging and, in the biomedical field, in vivo µCT allows researchers to make virtual 3D models of the skeleton and organs of live small animals. Three-dimensional models like these could provide insight into diseases and guide the development of medicines and therapies.

In vivo µCT holds three major advantages over other methods:

  1. It allows for repeated measurements of small live animals at different times without having to sacrifice them.
  2. It eliminates variation among individuals.
  3. It can reduce the number of animals required to obtain statistically meaningful data.

A variety of commercially available µCT scanners that are optimised for scanning live animals are now available. The use of in vivo µCT in ecological and evolutionary studies, however, has greatly lagged behind its use in biomedical studies. Continue reading

Scat Collection Protocols for Dietary DNA Metabarcoding

DNA dietary analysis is a non-invasive tool used to identify the food consumed by vertebrates. The method relies on identifying prey DNA in the target animals’ scats. It’s especially useful for marine animals such as seals and seabirds as it is difficult to watch their feeding events.

In the video below, Julie McInnes describes scat collection protocols that she (along with Rachael Alderman, Bruce Deagle, Mary-Anne Lea, Ben Raymond and Simon Jarman) developed to optimise the detection of food DNA in vertebrate scat samples. The authors use the shy albatross to demonstrate their new methods.

Continue reading

Testing the Effects of Underwater Noise on Aquatic Animals

Post provided by Karen de Jong

Most people assume that research equipment is expensive and complicated. But, it doesn’t need to be and the noise egg is a perfect example of this. It consists of a watertight container (as used by scuba divers) and the buzzer from a cellphone and does exactly what it says: it produces low frequency noise. This allows researchers to test the effect of noise on underwater life. It is a small, simple and cheap device that anyone can build.

Why Test Effects of Noise?

A painted goby in front of his nest ©K. de Jong

A painted goby in front of his nest ©K. de Jong

Underwater noise is rapidly increasing due to, for example, boat traffic and offshore wind farms. This can lead to stress for animals and difficulties in communication. Just as people have a hard time communicating in a noisy pub, animals may struggle to get their messages across when background noise is high. A nice description of how animals use sound and how noise may affect this can be found at www.dosits.org

While there is some knowledge on the effect of noise on large aquatic animals, we still know very little about how fish and other small aquatic animals are affected. Such knowledge is vital for management of protected areas. It’s also important to know whether wind farms and boat traffic can affect reproduction in populations of underwater resources such as fish and mussels. The answers to these questions are likely to be species specific, so we’ll need data on a large number of species in different habitats. Continue reading

Flawed Analysis Casts Doubt on Years of Evolution Research

Below is a press release about the Methods in Ecology and Evolution paper ‘‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data‘ taken from the University of Bristol.

Years of research on the evolution of ancient life, including the dinosaurs, have been questioned after a fatal flaw in the way fossil data are analysed was exposed by scientists from the universities of Reading and Bristol.

Studies based on the apparently flawed method have suggested Earth’s biodiversity remained relatively stable – close to maximum carrying capacity – and hinted many signs of species becoming rapidly extinct are merely reflections on the poor quality of the fossil record at that time.

However, new research by scientists at the University of Reading suggests the history of the planet’s biodiversity may have been more dynamic than recently suggested, with bursts of new species appearing, along with crashes and more stable periods.

Continue reading

Jellyfish Help Scientists to Fight Food Fraud

Below is a press release about the Methods paper ‘Stable isotope-based location in a shelf sea setting: accuracy and precision are comparable to light-based location method‘ taken from the University of Southampton.

©Katie St John Glew

©Katie St John Glew

Animals feeding at sea inherit a chemical record reflecting the area where they fed, which can help track their movements, according to a new study by scientists from the University of Southampton.

Chemical testing of the source of marine food products could be a powerful tool to help to fight food fraud, maintain healthy sustainable fish stocks or marine protected areas, and ensure consumer confidence in marine eco-labelling. Continue reading